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- PDB-2qlh: mPlum I65L mutant -

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Basic information

Entry
Database: PDB / ID: 2qlh
TitlemPlum I65L mutant
ComponentsFluorescent protein plum
KeywordsFLUORESCENT PROTEIN / far-red fluorescent protein / acylimine
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShu, X. / Remington, S.J.
CitationJournal: To be Published
Title: Structural Studies of Far-Red Emission in mPlum, a Monomeric Red Fluorescent Protein
Authors: Shu, X. / Wang, L. / Colip, L. / Kallio, K. / Remington, S.J.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein plum
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)51,2102
Polymers51,2102
Non-polymers00
Water8,485471
1
A: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6051
Polymers25,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6051
Polymers25,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.164, 77.419, 96.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fluorescent protein plum


Mass: 25604.912 Da / Num. of mol.: 2 / Mutation: I66L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q5S3G7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growpH: 8.5 / Details: 200mM NaCl, 100mM Tris pH8.5, 30% PEG 3400

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 36504

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Processing

Software
NameClassification
HKL-2000data collection
TNTrefinement
HKL-2000data reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G7K
Resolution: 1.9→10 Å
RfactorNum. reflection
Rfree0.279 -
Rwork0.182 -
all0.182 -
obs0.182 36504
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 0 472 3931

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